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- PDB-5fu2: The complexity of the Ruminococcus flavefaciens cellulosome refle... -

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Entry
Database: PDB / ID: 5fu2
TitleThe complexity of the Ruminococcus flavefaciens cellulosome reflects an expansion in glycan recognition
ComponentsCBM74-RFGH5
KeywordsSUGAR BINDING PROTEIN / CELLULOSOME / CARBOHYDRATE BINDING MODULE / RUMINOCCOCUS FLAVEFACIENS / ENDOGLUCANASE CEL5A
Function / homology: / Carbohydrate binding module-like / metal ion binding / Carbohydrate binding module
Function and homology information
Biological speciesRUMINOCOCCUS FLAVEFACIENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsBasle, A. / Luis, A.S. / Venditto, I. / Gilbert, H.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Complexity of the Ruminococcus Flavefaciens Cellulosome Reflects an Expansion in Glycan Recognition.
Authors: Venditto, I. / Luis, A.S. / Rydahl, M. / Schuckel, J. / Fernandes, V.O. / Vidal-Melgosa, S. / Bule, P. / Goyal, A. / Pires, V.M.R. / Dourado, C.G. / Ferreira, L.M.A. / Coutinho, P.M. / ...Authors: Venditto, I. / Luis, A.S. / Rydahl, M. / Schuckel, J. / Fernandes, V.O. / Vidal-Melgosa, S. / Bule, P. / Goyal, A. / Pires, V.M.R. / Dourado, C.G. / Ferreira, L.M.A. / Coutinho, P.M. / Henrissat, B. / Knox, J.P. / Basle, A. / Najmudin, S. / Gilbert, H.J. / Willats, W.G.T. / Fontes, C.M.G.A.
History
DepositionJan 20, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CBM74-RFGH5
B: CBM74-RFGH5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5988
Polymers23,6702
Non-polymers1,9296
Water3,045169
1
A: CBM74-RFGH5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6642
Polymers11,8351
Non-polymers8291
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CBM74-RFGH5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9356
Polymers11,8351
Non-polymers1,1005
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.623, 47.272, 83.958
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein CBM74-RFGH5


Mass: 11834.903 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RUMINOCOCCUS FLAVEFACIENS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A1A9TAF4*PLUS

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Sugars , 2 types, 2 molecules

#2: Polysaccharide beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D- ...beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose


Type: oligosaccharide / Mass: 828.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DManpb1-4DManpb1-4DManpb1-4DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a1122h-1b_1-5]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D- ...beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose


Type: oligosaccharide / Mass: 990.860 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DManpb1-4DManpb1-4DManpb1-4DManpb1-4DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,6,5/[a1122h-1b_1-5]/1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1WURCSPDB2Glycan 1.1.0
[][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{}}}}}}LINUCSPDB-CARE

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Non-polymers , 3 types, 173 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsSEQUENCE MAPS TO REGION IN GI:497670283

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 36 % / Description: NONE
Crystal growDetails: 200 MM CACL2 100 MM NA ACETATE PH 5.0 20% W/V PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97959
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97959 Å / Relative weight: 1
ReflectionResolution: 1.4→47.27 Å / Num. obs: 36544 / % possible obs: 100 % / Observed criterion σ(I): 1.5 / Redundancy: 7.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.4
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.98 / Mean I/σ(I) obs: 1.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5AOT

5aot


Resolution: 1.4→41.98 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.972 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.072 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ANISOTROPIC BFACTORS
RfactorNum. reflection% reflectionSelection details
Rfree0.19976 1866 5.1 %RANDOM
Rwork0.15799 ---
obs0.16019 34616 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.573 Å2
Baniso -1Baniso -2Baniso -3
1--1.1 Å20 Å20 Å2
2--0.37 Å20 Å2
3---0.73 Å2
Refinement stepCycle: LAST / Resolution: 1.4→41.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1513 0 139 169 1821
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191729
X-RAY DIFFRACTIONr_bond_other_d0.0020.021473
X-RAY DIFFRACTIONr_angle_refined_deg1.6362.0092375
X-RAY DIFFRACTIONr_angle_other_deg0.98433456
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1695195
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.1225.38578
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.32815241
X-RAY DIFFRACTIONr_dihedral_angle_4_deg3.868152
X-RAY DIFFRACTIONr_chiral_restr0.2020.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211835
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02387
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7191.574774
X-RAY DIFFRACTIONr_mcbond_other1.6981.572773
X-RAY DIFFRACTIONr_mcangle_it2.132.364965
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5061.817955
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.53533202
X-RAY DIFFRACTIONr_sphericity_free31.305569
X-RAY DIFFRACTIONr_sphericity_bonded11.5453246
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 112 -
Rwork0.254 2530 -
obs--99.92 %

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